VERSION RELEASES

[salvadord]

# Version 0.9.2

https://github.com/Neurosim-lab/netpyne ... tag/v0.9.2

- Support for saving simulation at intervals

- Improved Python cell template import so can read section names from a Python list or dict of sections

- Fixed replicability issue across different number of cores when using 'connList' connectivity rules

- Improved speed performance of 'connList' connectivity rules

- Updated RxD calcium buffering example

- Added netClamp example to re-simulate activity of single cell from network data

- Added support for recording and plotting variable time step

- Replaced spectrogram FFT method with Morlet wavelet method

- Updated installation instructions

- Added 'fontSize' argument to several plots

- Fixed issue completing batches in Python 3

- Fixed bug saving evolutionary optimization batch output file

- Fixed bug in plotShape()

- Fixed bug in plotSpikeStats()

- Fixed bug loading files with colons

- Fixed issue sorting raster by population and y coord

[salvadord]

# Version 0.9.3

https://github.com/Neurosim-lab/netpyne ... ag/v.0.9.3

- Improved conversion from SONATA format, including 300 biophys cell example

- Added saveCellConns, pt3dRelativeToCellLocation and invertedYCoord cfg options

- Added lineWidth as argument of plotRatePSD() and plotLFP()

- Modified plotLFP and plotRatePSD to use Morlet wavelet for PSD calculation

- Added lineWidth argument to some raster and LFP plots

- Added shuffling test to granger causality functions

- Fixed bug plotting traces with one fig per trace

- Fixed bug in granger functions - required conversion to int

- Fixed bug in plotShape when cells sections not available

- Return meaningful cell info via 'repr' and 'str' for pointCell, compartCell

- Fixed spelling typos in documentation

[salvadord]

# Version 0.9.4

https://github.com/Neurosim-lab/netpyne ... tag/v0.9.4

- Added option to avoid creating connections with weight=0

- Made recording of dipoles optional with attribute cfg.recordDipoles

- Rotated conn matrix x-axis labels so can fit large matrices

- Added 'removeWeightNorm' argument to plotConn() function

- Added cfg option 'oneSynPerNetcon' to conn rules to create one synapse object per Netcon

- Added first version of Contributors Guide

- Fixed file write permissions for evol optim batches

- Fixed bug calculating normally distributed rhythmic inputs - was using variance instead of std

- Fixed bug in iplotDipole when smoothing window size = 0

- Fixed bug in plotSpikeStats pop order

- Fixed bug is plots with scalebars

- Fixed bug in grid lines of plotConn

- Fixed bug in subConnParams by sorting conns to ensure reproducibility on different number of cores

- Fixed bug so uses 'Agg' backend if no display env variable e.g. in clusters

[salvadord]

# Version 0.9.5

https://github.com/Neurosim-lab/netpyne ... tag/v0.9.5

- Print start and end date/time

- Avoid removing batch folder so can rerun and complete batch simulations

- Added loadBalance option to print individual node computer times

- Initialize hoc events recursivley to reduce event queue overhead

- Added plotRateSpectrogram analysis function

- Added option to save at intervals

- Fixed bug: wrong indentation for initializing fixedInterval in batch.py

- Fixed bug in _distributeSynsUniformly function

- Fixed bug in subConnParams grouped synapses

- Fixed bug in analysis.granger figure save name

- Fixed bug in printRunTime function

[joe.w.graham]

# Version 0.9.6

https://github.com/Neurosim-lab/netpyne ... ag/v0.9.6

- Added useful hover information to iplots

- Improvements to iplotTraces

- Added interactive plot for connectivity (iplotConn)

- Added 'dynamicRates' option for NetStim populations

- Added option to have a uniform distribution of rates for Vecstim pulses

- Added function for distributed saving at intervals

- Added issue templates for GitHub

- Overhaul of contribution guide (CONTRIBUTING.md)

- Improved documentation

- Fixed bugs and improved exception handling in plotConn

- Fixed loadSave V1 example model

- Fixed bug calculating popRates when no spikes

- Fixed bug in _distributeSynsUniformly()

- Fixed bug in saveCellParamsRule()

- Fixed bug in batch.py: initCfg params were not being updated for evol optim

- Fixed bug in subconn.py: missing initialization of newWeightNorm

- Fixed bug in run.py: print run time with 2 significant figures

- Fixed output stat filenames of evolutionary optim: .cvs to .csv

- Fixed bug in interval saving

- Fixed bug in spikes.py in plotSpikeStats

[joe.w.graham]

We have released NetPyNE version 0.9.7, which includes some major improvements:

- All analyses functions can now generate interactive HTML plots (via Bokeh package)
- Online documentation and tutorials have been updated and expanded (see http://www.netpyne.org/)
- Simplified cell type specification to facilitate model building
- New parameter optimization methods: Adaptive Stochastic Descent and Optuna (see examples)

See github.com/Neurosim-lab/netpyne/blob/v0.9.7/CHANGES.md for a complete list of improvements.
See netpyne.org/install.html for instructions on installation or updating.

Additionally, we have released our new NetPyNE GUI (see fig below) with a more intuitive interface, better performance and new features. Try out the new NetPyNE GUI without installing any software at: netpyne.org/gui

To learn more please check out our Tutorial and Workshop at CNS'2020 (register for free at http://cnsorg.org/cns-2020):

Tutorial: "Building mechanistic multiscale models, from molecules to networks, using NEURON and NetPyNE", July 18; website: https://sites.google.com/neurosim.downs ... 0-tutorial

Workshop: "Tools and resources for developing and sharing models in computational neuroscience", July 21-22; website: https://neuralensemble.github.io/Networks_SIG/CNS2020

[joe.w.graham]

NetPyNE v0.9.8 is now available.

For a complete list of changes and bug fixes see: https://github.com/Neurosim-lab/netpyne ... tag/v0.9.8

See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html

NetPyNE Version 0.9.8

New features

- analysis.plotLFP can now be applied to external data

- Evolutionary and Optuna optimization can now read results from .pkl files

- Enabled recording of stimulus variables (e.g. SEClamp i)

- Added options in load func to avoid instantiating cells, conns, stims and/or rxd

- Analysis and plotting of rate vs current (f-I) curve for single cell tuning

- Recording and plotting of current dipoles in arbitrary subset of populations

- Added option to plot LFP spectrogram with log y-axis

- Added option to plot the log of connectivity in plotConn

- Enabled random distribution of multiple synapses with synsPerConn>1 and connRandomSecFromList=True

- Added lineWidth option to plot2Dnet (thanks Eric!)

- Updated Travis Continuous Integration to use NEURON 7.8.1 (from 7.6.2)

- Removed trailing white space from all Python files in the repository


Bug fixes

- Fixed bug when using index with recordTraces

- Fixed axes values in plotRxDConcentration and iplotRxDConcentration

- Added links to necessary mod files in the importing cell models tutorial

- Added aux_fun.inc to doc/source/code/mod as it's needed for some examples

- Blocked terminal output from Git when no repository is found (i.e. with pip install netpyne)

- Avoid adding section-based weightNorm values to point neurons (was affecting tut_import.py)

- Prevent error when loading pointCell params from json by converting Dict to dict

- Fixed bug in plotShape (thanks Eric!)

- Updated setup.py so PyPI website renders the README as markdown

- Fixed expected numSpikes in test of M1detailed example

- Merged GUI branch into development branch

- Fixed bug in iplotConn

- Fixed bug and coloring in iplotSpikeStats with different themes

[joe.w.graham]

NetPyNE v0.9.9.1 is now available. For a complete list of changes and bug fixes see:
https://github.com/Neurosim-lab/netpyne ... g/v0.9.9.1 and
https://github.com/Neurosim-lab/netpyne ... tag/v0.9.9

For instructions to install or update NetPyNE to the latest version: http://www.netpyne.org/install.html

New features

* Plot current source density (CSD) from local field potential (LFP) simulated data

* Additional customization of 3D shape plot: show voltage as color, change proportions, include axis labels

* Enable modifyConns based on properties of presynaptic neurons

* Replaced -np with -n so compatible for all commands: mpiexec/mpirun/srun

* Updated netrxd.py and network.py to include RxD's Parameter class, naming of States and Regions, and specification of Region geometries that do not require arguments like 'membrane' and 'inside'

* Improved recordTraces such that the cond 'gid' can accept a list of numbers as well as a single number

* Added a new tutorial going through use of NetPyNE with virtual environments and Jupyter notebooks

* Added cfg.use_fast_imem to enable recording membrane voltage via seg.i_membrane_

* Added swc import ability to importCell (and thus importCellParams)

* Batch now polls processes, prints their output and terminates them once completed

* Updated web documentation to explain importing SWC files and add Recording Configuration section

* Added link to Jupyter notebook tutorial and video to website front page

Bug fixes

* Made rate_b be positional instead of keyword argument in rxd multiCompartmentReaction

* Check if _morphSegCoords exists in population before using

* Fixed bug to avoid recursive creating of synMechs when loading with cfg.oneSynPerNetcon=True

* Fixed an issue with running rxd code twice

* Wait until all subprocesses have ended before completing mpi_bulletin batches

* Fixed repeated rxd simulation issue for rates and reactions

* Fixed pointNeuron spikePattern 'sync' option

* Fixed gathering of dipoles when running on multiple cores (uncommented lines that had been commented for debugging)

[joe.w.graham]

NetPyNE v1.0.0 is now available.

For a complete list of changes and bug fixes see: https://github.com/Neurosim-lab/netpyne ... tag/v1.0.0

See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html

New features

- Added wrapper for distributed saving; can now simply replace 'sim.gatherData()' with 'sim.gatherDataFromNodes()'

- Added distributed saving/loading ability (save/load data by MPI node)

- Allowed to specify 'cellModel' and point neuron params in netParams.cellParams (not only in netParams.popParams)

- Added cellsVisualizationSpacingMultiplier property to netParams

- Improved Granger plot, renamed it plotGranger

- Added interactive Granger plot (iplotGranger)

- Implemented testing in GitHub Actions with pytest (thanks Daniel!)

- Improved sim.clearAll such that it works even before a sim is run

- Properly formatted all module docstrings

Bug fixes

- Fixed bug in TupleToStr function

- Fixed broken links in tutorials

- Bokeh update required changing options from None to 'auto'

[joe.w.graham]

NetPyNE v1.0.1 is now available. For a complete list of changes and bug fixes see: https://github.com/Neurosim-lab/netpyne ... tag/v1.0.1

See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html

New features

- Added new plotting module with custom plotters

- Separated analysis.plotSpikeRaster into analysis.prepareRaster and plotting.plotRaster

- Separated analysis.plotSpikeHist into analysis.prepareSpikeData, analysis.prepareSpikeHist, plotting.plotSpikeHist and plotting.plotSpikeFreq

- Separated analysis.plotLFP into analysis.prepareLFP, analysis.preparePSD, analysis.prepareSpectrogram, plotting.plotLFPTimeSeries, plotting.plotLFPPSD, plotting.plotLFPSpectrogram, and plotting.plotLFPLocations

- Mapped old analysis.plots onto new ones

- Interfaced with LFPkit to enable recording/plotting of dipole current moments and EEG signals

- Added Current Source Density (CSD) analysis and plots

- Enabled selecting a subset of cells to save individual LFP signal from via cfg.saveLFPCells = [...]

- Added cfg.saveLFPPops to store LFP generated individually by each population

- Function to return batch parameter combinations (used for GUI)

- Added jupyter nb tutorials

- Added hippocampus CA3 model example

- Updated SONATA importing

- Improved distributed saving and interval saving (more robust)

- Added mapping of netParams values within cfg (used for batch sims in GUI)

- Extended Action tests to pull requests (not just push)


Bug fixes

- Fixed setting cfgMapping nested params when not string

- Fixed defineCellShapes when sec['hObj'] is not a h.Section()

- Fixed bug when using lognormal in string functions

- Added rxdmath to avoid RxD error

- Fixed bug in Tutorial 8 (batch)

- When saving to JSON wait until file exists before returning (to avoid exiting before saving finished)

[vbragin]

NetPyNE v1.0.3 is now available. For a complete list of changes and bug fixes see: https://github.com/Neurosim-lab/netpyne ... tag/v1.0.3

See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html

New features

- Added ability to load PointCell from saved network

- Added MultiPlotter class to allow plotting line data on multiple axes

- Added option to use separate axis for each PSD trace (set axis='multi')

- Added new Batch method named SBI (Simulation Based Inference) with example folder (sbiOptim)

- Added support for string functions in properties of cell mechanism, in cell geometry (in netParams.cellParams)

- Added support for string functions in synMech parameters

- Massive update of schemas (validator.py and setup.py)

- More control over POINTER variables through synMechParams (e.g. for gap junctions)

- Introduced cell variables in cellParams

- Added plotRateSpectrogram to utils.py

- Functions prepareCSD() and plotCSD() are now available

- Updated documentation on install and about


Bug fixes

- Fixed bug with loading CompartCell with custom mechanisms from saved network

- Fixed bug with accessing proper sim data file during batch parameters optimization

- Fixed bug where most batch optimization methods used to misname simulation output file

- Fixed bug in pop.py: "gridSpacing" is in the list of excludeTags

- Fixed bug in network.py: in the list "stimStringFuncParams" --> 'del' instead of 'delay', and removed 'i'

- Fixed bug in conn.py: included "params['preSec'] = connParam.get('preSec')" in gapJunctions

- Fixed bug in stim.py: 'Loc' with capital letter, for making 'synMechLocFactor'

- Fixed some misinformation in reference.rst about the subconn

- Fixed bug in dipole calculation units - changed from mA to uA

- Fixed bug in conditional logic when gathering LFP / dipoles

- Allow tuples to specify population's cells in 'include' for plotSpike

- Cleaned up optuna optim tutorial

[vbragin]

NetPyNE v1.0.4 is now available. For a complete list of changes and bug fixes see: https://github.com/Neurosim-lab/netpyne ... tag/v1.0.4

See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html

New features

- Added 'linewidth' as argument of plotting.plotSpikeHist()

- More detailed validation of netParams

- Save and load model in native NetPyNE format

- Converted most of examples to new NetPyNE model structure

- Complex stimulation ('rhythmic', 'evoked', 'poisson' and 'gauss') for VecStim created as pointCell (as a population rule)

- Codebase brought into compliance with PEP8 conventions

- Updates in NeuroML examples and tests

Bug fixes

- fixed handling filenames with multiple dots in `MetaFigure.saveFig()`

- Fixed readCmdLimeArgs() default arguments for backward-compatibility

- Cleaned up example models to drop some legacy/irrelevant params

- RxD module: Parameters defined before reactions + names given by default when missing (by the key)

- Analysis: try ... except call in plotDipole

- Save hObj of gap junction to connParams

- Removed duplicated or unused code from gridSearch()

- Fixes in batch utilities to make OS-agnostic

[vbragin]

NetPyNE v1.0.5 is now available. For a complete list of changes and bug fixes see: https://github.com/suny-downstate-medic ... tag/v1.0.5
See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html

New features

- Time series and PSD plots for current source density (CSD)

- Added colorbar to CSD plot

- Support for Sun Grid Engine HPC

- Extended sim.gatherData() with more optional arguments for flexibility

- Specify linear/log scale in `plotRatePSD()`

- Print more info about exceptions in plotting functions

- Check RxD specification for potential syntax issues

- Prevent zero population size in scaled-down models

- Better messages for validation errors

Bug fixes

- Fixed errors in plotting with sim.cfg.gatherOnlySimData=True

- Support saving and loading data in .mat and .hdf5 formats

- Multiple fixes in `plotRatePSD()` - popColors, fft, minFreq

- Fixed sync lines in `plotRaster()`

- Fixed performance issue in `plotConn()` with `groupBy='pop'` (default)

- Fixed `recordTraces` to not require more presicion than segment size (for stim and synMech)

[vbragin]

NetPyNE v1.0.6 is now available. For a complete list of changes and bug fixes see: https://github.com/suny-downstate-medic ... tag/v1.0.6
See here for instructions to install or update to the latest version: https://www.netpyne.org/documentation/installation

New features

- Raster plot colored by phase

- Examples based on the CA3 model using the 'colorbyPhase' option in the plotRaster

- API for loading .mod files selectively

- Ability to specify custom executor to run batch with (defaults to `sh`)

Bug fixes

- Fixed loading point cell params from legacy models (issue 607)

- Fix voltage movie tutorial

- Fix to automatically include netstims in the sim.allSimData object when plotRaster 'include' selects 'all'

- Fixed loading netParams in some scenarios (bug caused by srting functions pre-processing)

- Fix of `plotRaster` pops coloring if ordered not by gid

- Made cells diversity work with popParams based on `cellsList` and `gridSpacing`

- Fixed handling of output of `sim.create()` - was wrong order (credit: Kate Doxey)

- Fixed undeclared var `dpi` in `plotShape()`

- Fixes in batch utils

- Added some missing math functions to use with 'Functions as string' functionality

- Switch file copying method to shutil to be compatible over all operating systems (credit: Henrik Podeus)

[vbragin]

NetPyNE v1.0.7 is now available. For a complete list of changes and bug fixes see: https://github.com/suny-downstate-medic ... tag/v1.0.7
See here for instructions to install or update to the latest version: https://www.netpyne.org/documentation/installation

New features

- Introducing `batchtools` subpackage for parameters exploration and optimization
- Added progress-bar indicating network creation progress. Toggle the progress bar with cfg.progressBar
- cfg.connRandomSecFromList and cfg.distributeSynsUniformly can now be overriden in individual conn rule
- Added ability to use `sec`, `loc`, `preSec` and `preLoc` from list in connList-type connParams
- Updated tests.examples.utils to allow for dynamic pathing
- Dropped python2 support

Bug fixes

- Better handling of exceptions in `importCellParams()` (incl. `h.load_file()` - issue 782)
- Pandas deprecated parameter fix
- Fixed pointer id overflow on MPI (e.g. for gap junctions)
- preSec and preLoc are no longer lost for inverse pointer connection
- Fixed crash due to use of matplotlib.TextArea deprecated param (credit: Christian O'Reilly)
- syncLines in rasterPlot restored
- Fixed a bug in `gatherDataFromFiles()` where cellGids for node 0 were lost
- Fixed generating rhythmic spiking pattern with 'uniform' option
- Fixed misleading console output when cfg.recordStims is On
- The colors in CSD plots are now properly aligned vertically with the CSD time-series overlays (credit: Sam Neymotin)
- Update mkdir to makedirs (credit: Jacob Sprouse)